We examined the density, size and species distribution of groupers in three habitats on an inshore-to-offshore transect across Elbow Reef, Florida Keys: high-relief spur-and-groove (4–9 m depth), relict spur-and-groove (10–20 m), and deep fore reef slope (21–30 m). Physical relief was greatest in the high-relief spur-and-groove (up to 3 m), lowest in the relict spur-and-groove habitat (30%). There were significant differences in the density, size, and species distribution of groupers among the three habitats. Graysby, Epinephelus cruentatus, was numerically dominant, constituting 82–91% of individual observed. Black grouper, Mycteroperca bonaci, and Nassau grouper, E. striatus, were more abundant in high to moderate relief habitats, whereas red hind, E. guttatus, was more abundant in the low-relief habitat. The size distribution was shifted towards smaller sizes in lowest relief habitat and towards larger sizes in areas with greater (>0.5 m) vertical relief. We suggest that fishing pressure in the Florida Keys has resulted in an offshore grouper assemblage dominated by graysby, a small grouper species (length) which is not targeted by fishermen, and that habitat selection and biological interactions have significantly influenced the ecological structure of the grouper assemblage of this coral reef.